[2020-03-09 06:53:04] Beginning TopHat run (v2.1.1)
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[2020-03-09 06:53:04] Checking for Bowtie
		  Bowtie version:	 2.3.4.1
[2020-03-09 06:53:05] Checking for Bowtie index files (genome)..
[2020-03-09 06:53:05] Checking for reference FASTA file
[2020-03-09 06:53:05] Generating SAM header for Bowtie2Index/genome
[2020-03-09 06:53:09] Reading known junctions from GTF file
[2020-03-09 06:53:11] Preparing reads
	 left reads: min. length=75, max. length=75, 24097162 kept reads (12411 discarded)
[2020-03-09 06:57:59] Building transcriptome data files /scratch/3763321.1.p16/tophat2/tmp/RefSeq_GeneBody
[2020-03-09 06:58:08] Building Bowtie index from RefSeq_GeneBody.fa
[2020-03-09 07:02:11] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2020-03-09 07:08:35] Resuming TopHat pipeline with unmapped reads
[2020-03-09 07:08:35] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2020-03-09 07:15:54] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/3)
[2020-03-09 07:16:46] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/3)
[2020-03-09 07:17:36] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/3)
[2020-03-09 07:18:19] Searching for junctions via segment mapping
[2020-03-09 07:20:02] Retrieving sequences for splices
[2020-03-09 07:21:02] Indexing splices
[2020-03-09 07:21:16] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/3)
[2020-03-09 07:21:30] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/3)
[2020-03-09 07:21:43] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/3)
[2020-03-09 07:21:54] Joining segment hits
[2020-03-09 07:23:14] Reporting output tracks
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[2020-03-09 07:39:22] A summary of the alignment counts can be found in /scratch/3763321.1.p16/tophat2/align_summary.txt
[2020-03-09 07:39:22] Run complete: 00:46:17 elapsed